Genetic susceptibilities for breast cancer can be elucidated by studying genotype-phenotype correlates. This study investigated women from high risk breast cancer families, a sporadic breast cancer case-control study and associations for specific BRCA1 SNPs and haplotypes, Rad51 SNPs, and deficient DNA repair. The mutagen sensitivity assay, used to measure DNA repair capacity, was used to test associations with genotypes and haplotypes. Positive associations were then tested as predictors of breast cancer risk in a population-based case control study. BRCA1 carriers with breast cancer had more mean breaks per cell (MBPC) than BRCA1 carriers without breast cancer. An association was found for the Rad51 5'UTR 135C allele and MBPC (OR=3.40 95% CI: 1.20-9.90). There also was an increased risk for high MBPC with the BRCA1 D693N allele (OR=6.03 95% CI: 0.69-52.02; p=0.10). There was no association with for the BRCA1 Q356R and E1038G genotypes or haplotypes. The Rad51 5'UTR 135C allele was examined in a population-based case-control study of breast cancer, but no association was found. The results indicated that the Rad51 5'UTR 135C allele and maybe the D693N allele are modifying genotypes for the penetrance of BRCA1 mutation carriers, and so might only be risk factor for high risk families.